San Francisco’s $1.6 billion Central Subway project, already a year behind schedule, is facing a new challenge.

John Funghi, the Municipal Transportation Agency engineer who has overseen the big dig for 11 years, has been recruited to honcho Caltrain’s $1.9 billion conversion of its rail service from diesel to electric trains. He starts in February.

As for Funghi’s replacement?

“We will be posting the job,” said transportation agency spokesman Paul Rose, though he could not offer a timeline for it to be filled.

“It’s a bittersweet decision to leave,” said Funghi, who told us he will help out with the transition. “But it was just too good an opportunity to pass up ... building the spine to get commuter rail into downtown San Francisco.”

The Central Subway, a 1.7-mile extension of the T-Third Street line running from Fourth and Townsend streets to Chinatown, is about two-thirds finished. The scheduled opening date, however, is up for debate.

The subway’s main contractor, Tutor Perini Corp., recently told the Board of Supervisors that the line won’t be ready for passenger service until spring 2021 — nearly 2½ years after the original target date.

The city maintains the line will be completed by December 2019.

Tutor Perini has also submitted change order claims for the Central Subway that total $112 million. That exceeds the city’s contingency fund for the project by $33 million. [Read the full story at SFGATE]